9ju0 | pdb_00009ju0

C-terminally truncated dextran dextrinase bound with acarbose

spinqualitylabelsall models 9ju0, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9ju0 is a 4 chain structure with sequence from Gluconobacter oxydans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.5Å Ligands: AC1, CIT, EDO, GLC, PRD_900007 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A0M5MSC0_GLUOY Publication Abstract from PubMed Bacterial exopolysaccharide, dextran, primarily composed of alpha-(1-->6)-linked d-glucosyl residues, is synthesized from alpha-(1-->4)-glucan dextrin or sucrose through successive anomer-retaining transglucosylation reactions by dextran dextrinase (DDase) or dextransucrase, respectively. Although the structure-function relationship of dextransucrase has been extensively studied, that of DDase remains largely unknown. Herein, we revealed the Gluconobacter oxydans DDase structural basis through biochemical and structural analyses. The DDase comprises 1284 residues, with its N-terminal 902 residues being functionally essential. Crystal structure analysis of the minimal active DDase (Delta382C) complex with the pseudo-maltotetraose inhibitor, acarbose, revealed its homodimeric structure. A Delta382C protomer contains two beta-sandwich domains, N1 and N2, and an (alpha/alpha)(6)-barrel domain A. Surprisingly, domains N2, A, and the helix-loop-helix connecting them structurally resemble those of bacterial anomer-inverting glucohydrolases in glycoside hydrolase family 15 (GH15). Domain N1 primarily forms intra- and inter-subunit domain interfaces. The DDase acarbose-binding residues in subsite -1 are conserved with GH15 glucohydrolases. The DDase Glu671 and Glu858 are positioned similarly to the GH15 glucohydrolase general acid and base catalysts, respectively. However, Glu858 is approximately 1.2 to 1.6 A closer to the acarbose equivalent anomeric carbon, facilitating its role as a nucleophilic catalyst in the double displacement mechanism. The catalytic residue functions were biochemically confirmed using mutant enzymes. Spatial position of Glu858 is arranged by the local structure of the alpha11-->alpha12 loop and subunit interactions involving domain N1. Enzymes classified in the same GH family catalyze reactions with different mechanisms, anomer-inverting or -retaining, due to differences in their catalytic residue spatial arrangement. Structural basis of transglucosylation in dextran dextrinase, a homolog of anomer-inverting GH15 glucoside hydrolases.,Tagami T, Saburi W, Sadahiro J, Kumagai Y, Lang W, Matsugaki N, Okuyama M, Mori H, Kimura A J Biol Chem. 2025 Jul 30;301(9):110541. doi: 10.1016/j.jbc.2025.110541. PMID:40749827 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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